Rsubread

This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see Rsubread.

Rsubread: a super fast, sensitive and accurate read aligner for mapping next-generation sequencing reads

Bioconductor version: 2.8

This package provides an R interface to the Subread aligner (http://sourceforge.net/projects/subread/) for mapping next-gen sequencing reads. Subread aligns reads to the referenc genome by using a set of substrings(subreads) extracted from each read. The consensus location mapped by subreads directly determines the mapping location of the read. Therefore, there is no costly extension step as in the "seed-and-extend" mapping paradig. Subread achieves much higher mapping speed and mapping sensitivity than "seed-and-extend" aligners at no cost to the accuracy. Subread aligner can align reads from all the major platforms inculding Illumina GA/HiSeq, ABI SOLiD, Roche 454 and HeliScope. It supports the mapping of paired-end reads and it also allows a large number of indels in the mapping. It can be used to align long reads (>200bp) as well.

Author: Wei Shi, Yang Liao and Jenny Zhiyin Dai

Maintainer: Wei Shi <shi at wehi.edu.au>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Rsubread")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Rsubread")

Details

Package Archives

Follow Installation instructions to use this package in your R session.